| Second Harvest Food Bank of Santa Clara and San Mateo CountiesEIN 94-2614101 | Human Services | CA | $125,127,781Large | 97.68 |
| Second Harvest Food Bank Santa Cruz CountyEIN 77-0326685 | Human Services | CA | $19,193,561Large | 92.74 |
| Second Harvest Foodbank of Southern WisconsinEIN 39-1490691 | Human Services | WI | $33,052,619Large | 96.55 |
| Second Harvest Foodbank of the Mahoning ValleyEIN 34-1380074 | Human Services | OH | $17,272,324Large | 98.06 |
| Second Harvest HeartlandEIN 23-7417654 | Human Services | MN | $138,115,853Large | 85.05 |
| Second Harvest Inland NorthwestEIN 23-7173826 | Human Services | WA | $104,702,103Large | 93.32 |
| Second Harvest Northern Lakes Food BankEIN 36-3479964 | Human Services | MN | $10,915,737Mid-sized | 94.46 |
| Second HelpingsEIN 35-1484281 | Human Services | IN | $6,711,056Mid-sized | 98.23 |
| Second NatureEIN 04-3195772 | Environment | MA | $1,691,248Small | 89.82 |
| Second Stage TheatreEIN 13-3021180 | Arts, Culture, Humanities | NY | $9,254,856Mid-sized | 77.08 |
| Second StoryEIN 54-0899463 | Human Services | VA | $3,085,749Small | 91.02 |
| SECOREIN 20-4226894 | Human Services | CO | $4,048,217Mid-sized | 72.61 |
| Securing America's Future EnergyEIN 20-1727977 | Research and Public Policy | DC | $6,080,643Mid-sized | 74.06 |
| Sedgwick County Zoological SocietyEIN 48-6120530 | Animals | KS | $11,658,916Mid-sized | 90.32 |
| Seed Savers ExchangeEIN 43-1214133 | Environment | IA | $5,385,772Mid-sized | 84.73 |
| Seeds of Hope Charitable TrustEIN 84-1437053 | Education | CO | $2,367,910Small | 100.00 |
| Seeds of PeaceEIN 52-1814447 | International | NY | $5,723,593Mid-sized | 79.84 |
| SEG FoundationEIN 73-1329755 | Education | OK | $2,969,212Small | 85.10 |
| Segerstrom Center for the ArtsEIN 23-7287150 | Arts, Culture, Humanities | CA | $69,295,404Large | 89.82 |
| Self Enhancement, Inc.EIN 93-1086629 | Human Services | OR | $16,850,558Large | 86.57 |
| Senator John Heinz History Center- Historical Society of Western PennsylvaniaEIN 25-0965391 | Arts, Culture, Humanities | PA | $11,115,252Mid-sized | 90.62 |
| Seneca Park Zoo SocietyEIN 16-0905390 | Animals | NY | $5,429,091Mid-sized | 81.24 |
| Senior ConcernsEIN 95-2992927 | Human Services | CA | $1,864,713Small | 84.52 |
| Senior Link MidlandEIN 75-1899190 | Human Services | TX | $2,885,630Small | 90.74 |
| Senior NeighborsEIN 23-7195491 | Human Services | MI | $3,594,979Mid-sized | 94.69 |
| Senior ServicesEIN 56-1085968 | Human Services | NC | $6,935,007Mid-sized | 95.38 |
| Senior Services Inc. of WichitaEIN 48-0757988 | Human Services | KS | $2,430,872Small | 86.19 |
| Sephardic Food Fund EIN 56-2307777 | Human Services | NY | $2,663,245Small | 61.26 |
| SergeEIN 23-2223692 | Religion | PA | $14,401,712Large | 96.81 |
| SeriousFun Children's NetworkEIN 31-1794455 | Health | CT | $14,274,438Large | 91.85 |
| Serviam Girls AcademyEIN 26-0792594 | Education | DE | $864,712Small | 70.00 |
| Service Over SelfEIN 62-1760415 | Human Services | TN | $1,554,211Small | 84.96 |
| SETI InstituteEIN 94-2951356 | Research and Public Policy | CA | $20,609,248Large | 87.01 |
| Settlement Music SchoolEIN 23-1352676 | Education | PA | $10,681,642Mid-sized | 90.42 |
| Seva FoundationEIN 38-2231279 | International | CA | $7,518,689Mid-sized | 92.27 |
| Several Sources SheltersEIN 22-2368937 | Human Services | NJ | $2,363,897Small | 93.65 |
| Sewa International, IncEIN 20-0638718 | International | TX | $2,137,807Small | 100.00 |
| Sexual Assault CenterEIN 62-1043294 | Human Services | TN | $2,597,107Small | 91.17 |
| SFFILMEIN 94-2663216 | Arts, Culture, Humanities | CA | $6,042,427Mid-sized | 87.22 |
| SFJAZZEIN 94-2990335 | Arts, Culture, Humanities | CA | $16,924,582Large | 84.54 |
| Shake-A-Leg MiamiEIN 65-0611917 | Education | FL | $2,152,655Small | 83.20 |
| Shakespeare & CompanyEIN 04-2666826 | Arts, Culture, Humanities | MA | $4,795,855Mid-sized | 82.41 |
| Shakespeare Theatre CompanyEIN 52-1405988 | Arts, Culture, Humanities | DC | $21,930,518Large | 87.67 |
| Shalom AustinEIN 74-1469465 | Human Services | TX | $13,606,228Large | 85.00 |
| Shalom FoundationEIN 95-4894733 | International | TN | $830,312Small | 85.00 |
| Shane's InspirationEIN 95-4760497 | Human Services | CA | $2,205,495Small | 83.43 |
| ShantiEIN 94-2297147 | Health | CA | $4,966,512Mid-sized | 86.47 |
| SHAREEIN 13-3131914 | Health | NY | $1,754,882Small | 91.66 |
| Share & Care FoundationEIN 22-2458395 | International | NJ | $1,801,384Small | 94.79 |
| Share Our SelvesEIN 95-3222316 | Human Services | CA | $17,655,264Large | 90.63 |
| Share Our StrengthEIN 52-1367538 | Human Services | DC | $51,056,766Large | 80.07 |
| Shared Harvest FoodbankEIN 31-1096571 | Human Services | OH | $9,251,021Mid-sized | 86.64 |
| Shared Hope InternationalEIN 91-1938635 | International | WA | $3,062,526Small | 90.90 |
| Shared InterestEIN 13-3836581 | International | NY | $2,086,363Small | 89.75 |
| Sharing and Caring HandsEIN 36-3412619 | Human Services | MN | $8,873,662Mid-sized | 61.86 |
| Sharing ConnectionsEIN 36-4363123 | Human Services | IL | $2,816,731Small | 90.62 |
| Sharing HouseEIN 56-1292875 | Human Services | NC | $1,429,960Small | 89.52 |
| Sharon Lynne Wilson Center for the ArtsEIN 39-1787648 | Arts, Culture, Humanities | WI | $2,952,831Small | 78.38 |
| SharsheretEIN 13-4198529 | Health | NJ | $2,330,300Small | 99.43 |
| Shedd AquariumEIN 36-2167918 | Animals | IL | $59,336,621Large | 90.86 |